Soil disinfection is an important agronomic measure to prevent soil-borne diseases, insects, weeds and other hazards. Based on the premise of being environmentally friendly, microwave soil disinfection can improve crop yield and quality in a pollution-free, residue-free and green way. The law of microwave soil heating is the theoretical basis of microwave soil disinfection. Therefore, in this paper, loess soil of North China and black soil of Northeast China are used as test materials to explore the law of soil heating under the action of microwaves. First, COMSOL Multiphysics software was used to simulate the temperature field change in the microwave-irradiated soil, and a simulation model of the temperature field of the microwave-irradiated soil was constructed to analyze the effective working range and temperature distribution characteristics of the microwave-irradiated soil. Second, using the 2.45 GHz microwave treatment, the following conditions were tested: soil moisture conditions of 10%, 15%, 20% and 23% (within the natural moisture content range). The loess and black soil were treated by microwave irradiation for 1~12 min, respectively (1 min/time increment). A single-factor experiment was designed to explore the influence of these factors on the soil heating law. The results show that the two soil surface temperatures are positively correlated with the soil moisture content, both of which satisfy Tsurface23% > Tsurface20% > Tsurface15% > Tsurface10%, and the surface temperature of black soil is higher than that of loess. According to the experimental results of the internal temperature distribution of loess and black soil irradiated by microwaves, the surface equations of “irradiation time–soil depth-soil temperature” and “irradiation time–soil moisture content–soil temperature” were constructed by surface fitting. When the irradiation time and moisture conditions are the same, the average temperature inside the irradiation area satisfies T¯α black soil > T¯α loess. The results of long-term microwave soil heating preliminarily confirmed the feasibility of microwave soil disinfection and the optimal conditions of microwave irradiation in loess of North China and Northeast black soil, which provides a certain reference for the study of soil-borne diseases inactivation at high temperature.